Contacts of the strand formed by residues 510 - 520 (chain B) in PDB entry 3HIG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 510 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552A PRO* 5.7 2.0 - - - -
357B ALA* 4.7 2.2 - - + -
358B LEU 3.0 19.1 - - - +
359B TYR* 3.4 34.5 - + + -
461B TPQ 3.1 9.2 + - - -
485B VAL* 5.3 2.7 - - + -
486B HIS 5.7 1.1 - - - -
508B ASN 2.8 24.2 + - - -
509B ILE* 1.3 79.9 - - - +
511B THR* 1.3 59.8 + - - +
512B HIS* 3.4 17.9 - + - -
674B LEU* 3.4 6.0 - - - +
675B HIS* 2.7 56.9 + + + +
677B PRO* 3.9 9.0 - - + -
801B CU 2.1 32.8 - - - -
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Residues in contact with THR 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534A MET* 4.7 5.0 - - - +
552A PRO* 6.1 0.7 - - - +
356B VAL 3.7 1.2 - - - +
357B ALA* 3.4 3.8 - - - -
358B LEU* 2.9 34.8 + - - +
510B HIS* 1.3 76.3 - - - +
512B HIS* 1.3 72.4 + - - +
513B LEU* 4.0 13.2 + - + +
601B ALA* 5.5 3.6 - - - -
602B ASP 5.4 1.8 - - - +
604B VAL* 3.7 39.8 - - + +
673B PHE* 3.4 19.5 - - - +
674B LEU* 3.6 16.9 - - + +
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Residues in contact with HIS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B VAL 3.3 6.9 + - - +
357B ALA* 4.4 6.0 - - + +
461B TPQ 3.6 21.5 - + - -
463B TYR* 3.0 36.6 + + - -
479B MET* 5.4 4.9 - - + +
481B ALA* 4.9 2.4 - - + +
510B HIS* 3.1 12.0 + + - -
511B THR* 1.3 74.9 - - - +
513B LEU* 1.3 64.0 + - - +
514B VAL* 5.5 3.1 - - + -
672B GLY* 3.0 5.7 - - - -
673B PHE* 3.0 73.9 + + + +
675B HIS* 3.7 3.1 + - + -
801B CU 2.0 31.9 - - - -
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B ALA* 3.5 1.7 - - - -
356B VAL* 2.8 38.6 + - + +
358B LEU* 4.1 26.2 - - + -
511B THR* 4.0 13.9 + - + +
512B HIS* 1.3 82.2 - - - +
514B VAL* 1.3 62.4 + - - +
569B PHE* 5.3 0.7 - - + -
601B ALA* 3.7 29.2 - - + -
602B ASP 4.5 7.6 - - - +
604B VAL* 4.2 11.4 - - + +
615B ILE* 4.8 2.2 - - + -
617B TRP* 4.0 16.6 - - + -
618B ALA* 3.6 25.4 - - + -
670B THR* 4.1 11.9 - - + -
671B VAL 3.6 2.2 - - - -
672B GLY* 4.4 0.7 - - - -
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Residues in contact with VAL 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B VAL* 4.8 1.6 - - + -
354B GLU 3.3 11.2 - - - +
355B ALA* 4.3 7.9 - - + -
463B TYR* 6.2 1.8 - - + -
465B TRP* 3.8 30.1 - - + -
479B MET* 4.3 22.7 - - + -
512B HIS* 5.5 2.9 - - + -
513B LEU* 1.3 79.7 - - - +
515B HIS* 1.3 64.7 + - - +
516B TYR* 3.6 28.7 - - + -
617B TRP* 4.0 3.4 - - - -
669B VAL 3.7 0.9 - - - +
670B THR* 3.4 5.2 - - - +
671B VAL* 2.8 43.9 + - + +
672B GLY* 5.9 0.2 - - - -
692B VAL* 5.1 0.9 - - + -
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Residues in contact with HIS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B VAL* 3.9 2.3 - - - -
353B GLN* 2.8 36.8 + - + +
354B GLU 2.9 12.8 + - - +
514B VAL* 1.3 75.8 - - - +
516B TYR* 1.3 56.3 + - - +
617B TRP* 3.4 48.1 + + + +
620B TYR* 5.0 1.2 + - - +
634B SER* 2.8 23.4 + - - +
650B PHE* 4.1 4.5 - + - -
668B TRP* 3.4 46.6 - + + +
669B VAL 3.2 17.3 + - - -
670B THR* 3.3 20.5 + - - -
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Residues in contact with TYR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B SER* 3.3 21.1 - - - +
352B VAL* 3.9 18.8 - - + -
353B GLN* 4.0 3.6 - - - -
465B TRP* 3.6 20.6 - + - -
466B ASP 5.1 0.3 + - - -
467B PHE* 4.3 10.5 - + - -
477B ALA* 3.9 17.0 - - + -
478B LYS* 3.9 21.8 + - - -
479B MET* 4.1 2.9 + - + +
514B VAL* 3.6 25.4 - - + -
515B HIS* 1.3 75.0 - - - +
517B ARG* 1.3 59.9 + - - +
518B VAL* 4.0 7.3 + - + +
668B TRP* 3.4 8.5 - - - +
669B VAL* 2.9 38.3 + - + +
671B VAL* 4.1 18.6 - - + -
693B GLY* 5.0 3.4 - - - -
694B PHE* 3.6 34.3 - + + -
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Residues in contact with ARG 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLU* 2.9 35.4 + - - +
350B VAL* 3.4 4.7 - - - +
351B SER* 2.8 34.4 + - - +
353B GLN* 3.5 22.1 - - + +
516B TYR* 1.3 72.5 - - - +
518B VAL* 1.3 63.9 + - - +
519B ASP* 4.4 6.7 + - - +
627B TYR* 3.3 37.2 - - - +
628B ARG 5.0 1.2 + - - +
631B GLU 3.0 24.9 + - - -
632B LEU* 3.2 34.5 + - - +
666B VAL* 3.8 24.3 - - + +
667B ALA 3.9 2.0 - - - -
668B TRP* 3.1 29.4 - - + -
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Residues in contact with VAL 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B GLU 3.7 2.0 - - - -
350B VAL* 4.2 10.1 - - + +
516B TYR* 4.3 4.5 - - + +
517B ARG* 1.3 78.7 - - - +
519B ASP* 1.3 56.9 + - - +
520B LEU* 3.1 35.7 + - + +
595B LEU* 5.6 0.9 - - + -
666B VAL* 4.2 1.1 - - - -
667B ALA* 2.7 47.8 + - + +
669B VAL* 4.0 20.2 - - + -
694B PHE* 3.6 28.7 - - + -
696B LEU* 4.1 20.2 - - + -
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Residues in contact with ASP 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 2.9 23.5 + - - -
347B ALA* 3.4 1.8 - - - -
348B TYR* 2.7 48.6 + - - +
349B GLU* 2.7 28.9 + - + +
517B ARG* 3.9 8.7 + - - +
518B VAL* 1.3 69.0 - - - +
520B LEU* 1.3 54.0 - - - +
521B ASP* 3.2 1.1 - - - +
627B TYR* 3.8 10.1 - - - -
664B ASP* 3.5 1.2 - - - +
665B LEU 3.2 4.9 - - - +
666B VAL* 3.8 21.6 - - + +
802B CA 2.3 31.7 - - - -
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Residues in contact with LEU 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ILE* 3.4 16.2 - - + +
347B ALA* 3.8 14.1 - - + +
518B VAL* 3.1 20.7 + - + +
519B ASP* 1.3 73.1 - - - +
521B ASP* 1.3 55.1 + - - +
522B VAL* 3.8 13.0 - - + -
527B ASN* 3.6 7.4 - - - +
579B PHE* 3.6 46.2 - - + -
593B TYR* 5.0 7.4 - - + +
595B LEU* 6.2 0.2 - - + -
665B LEU* 3.5 5.4 + - - +
667B ALA* 5.2 2.0 - - + +
696B LEU* 3.7 43.3 - - + -
802B CA 2.4 26.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il